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anonymoUUs

Python package to replace identifiable strings in multiple files and folders at once

de-identification
python
text

Python
Jupyter Notebook

Baklava

Deploys a Kubernetes cluster and big data services on the cloud.

Big data
High performance computing
Optimized data handling

Python
HCL
Dockerfile
+ 2

BenchmarkRecovery

This project simulates Landsat data and evaluates the performance of recovery indicators with respect to data and disturbance characteristics.

BIRCH

BIRCH is a powerful framework for organizing and using bioinformatics. BIRCH comes with hundreds of commonly-used tools, and allows you to customize your BIRCH site by adding new ones.

bioinformatics
BLAST
genomics
+ 3

BrainBrowser

BrainBrowser is an open source JavaScript library exposing a set of web-based 3D visualization tools primarily targetting neuroimaging

3D
brainbrowser
neurology
+ 2

JavaScript
Python
CSS
+ 1

byteparsing

Parser library for reading custom binary files from Python.

Big data
Multi-scale & multi model simulations
Optimized data handling

Jupyter Notebook
Python
C++
+ 5

CBRAIN

CBRAIN is a flexible Ruby on Rails framework for accessing and processing of large data on high-performance computing infrastructures.

CBRAIN
cluster
Data Analysis
+ 6

Ruby
HTML
JavaScript
+ 3

ChemTools

ChemTools is a free and open source Python library for interpreting the results of quantum chemistry calculations.

atoms in molecules
conceptual dft
density matrices kinetic energy density
+ 2

Python

dCacheFS

Python file-system interface for dCache storages.

Data
Inter-operability & linked data
Optimized data handling
+ 1

Python
Jupyter Notebook

Emo-spectre

Interactive visualization and exploration of multi modal time-series data and video

Visualization
Workflow technologies

PLpgSQL
Vue
JavaScript
+ 5

emvoice

A Python package for computing emotion expression-related features from speech signals.

Emotion expressions
python
Speech processing

Python
Shell

FAIRSECO

FAIRSECO provides a way to quickly analyse a variety of data and metrics of your software, and it allows you to explore the impact of your software on the academic world. Metadata is gathered from many different sources, which is then analysed and compiled into a clear overview.

Data Analysis
FAIR
Inter-operability & linked data
+ 2

TypeScript
EJS
JavaScript

Lysander

Find people on Twitter given a small initial set of interesting people.

Text analysis & natural language processing

Python

GameBus FHIR Layer

Enable FHIR service for GameBus and beyond

Data Harmonization
FHIR
healthcare
+ 1

Java
Dockerfile
Shell

Geodisy

Geodisy is a research data discovery tool that harvests information from existing research data repositories and displays applicable records onto a map-based search interface.

geospatial
metadata
research data

Java
Ruby
XSLT
+ 6

GridFormat

Header-only C++ Library for grid file I/O

Grid-based PDE methods
grid file I/O
mesh file I/O
+ 3

C++
CMake
Python
+ 1

IRIDA

Integrated Rapid Infectious Disease Analysis (IRIDA) platform is a user-friendly, distributed, open source bioinformatics and analytical web platform that was developed to support real-time infectious disease outbreak investigations using whole genome sequencing data.

genomics
infectious disease

Java
JavaScript
TypeScript
+ 6

ISAAC Chrome extension

Chrome Web Extension for support of the NWO ISAAC platform. This extension is not endorsed or developed by the NWO.

BibTeX
CITATION.cff
DataCite
+ 1

JavaScript
HTML
CSS
+ 1

i-VRESSE workflow-builder

Need to write a complex config file then the i-VRESSE workflow builder might be the tool for you.

Workflow technologies

TypeScript
Python
CSS
+ 3

LORIS

Longitudinal Online Research and Imaging System (LORIS) is a web-based data and project management software for neuroimaging research studies. It is an OPEN SOURCE framework for storing and processing behavioural, clinical, neuroimaging and genetic data.

Computational Neuroscience
database
neuroimaging
+ 3

PHP
JavaScript
TypeScript
+ 9

Mahiru

A prototype for a federated, distributed data sharing and processing system.

Data processing
Data Sharing
Policies
+ 1

Python
Makefile
Dockerfile
+ 2

Massive PotreeConverter

Use parallel processing to quickly convert large point cloud data sets to the format used by the Potree viewer.

Big data
Optimized data handling

Python

Mass Spec Studio

A user-friendly, fully extensible framework for mass spectrometry analysis.

mass spectrometry
proteins

MMSODA Toolbox for MATLAB

MATLAB toolbox for global optimization and state estimation of dynamic models using distributed computing.

HTML
MATLAB
TeX
+ 5

Motus Wildlife Tracking System

The Motus Wildlife Tracking System (Motus) is an international collaborative research network that uses coordinated automated radio telemetry to facilitate research and education on the ecology and conservation of migratory animals.

conservation science
movement ecology
wildlife tracking

mzRecal

mzRecal recalibrates mass spectrometry (MS1) data in mzML format, using peptide identifications in mzIdentML.

mass spectrometry
proteomics

Go
Shell
R
+ 2

NPLinker

Microbial natural products data mining by integrating genomics and metabolomics data

Data processing
multi-omics integration

Python
TeX
Shell
+ 2

Open Computational Multiphysics

OpenCMP is a computational multiphysics software package based on the finite element method

Computational Fluid Dynamics (CFD)
computational Multiphysics
diffuse interface method
+ 3

Python
TeX

OpenMS

OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software. OpenMS is free software available under the three clause BSD license and runs under Windows, macOS, and Linux.

C++
mass spectrometry
metabolomics
+ 1

C++
MAXScript
Cython
+ 15

OpenPNM

OpenPNM is an open source project aiming to provide porous media researchers with a ready-made framework for performing a wide range of pore network simulations.

Pore network modeling

C++
MAXScript
Cython
+ 15

openPSTD

openPSTD is a Python-based research software that allows efficient and detailed calculation of sound propagation in a 2D built environment. It is especially useful as a reference tool for other developed software on acoustic sound propagation.

Acoustics
GPU
python

C++
C
GLSL
+ 3

PAVICS

PAVICS is a virtual laboratory facilitating the analysis of climate data. It provides access to several data collections ranging from observations, climate projections and reanalyses. It also provides a Python programming environment to analyze this data without the need to download it.

analysis
climate
Climate change
+ 5

HTML
Jupyter Notebook
Python
+ 3

PhenoTips

PhenoTips is a software tool that makes it easy for clinicians and researchers to draw pedigrees and collect structured phenotype data for patients with genetic disorders.

API
deep phenotyping
genogram
+ 6

Java
JavaScript
HTML
+ 4

Plus Toolkit

Toolkit for data acquisition, pre-processing, calibration, and real-time streaming of imaging, position tracking, and other sensor data for medical applications.

3D Slicer
electromagnetic tracking
image capture
+ 7

C++
C
CMake
+ 2

PoreSpy

PoreSpy is a collection of image analysis tools used to extract information from 3D images of porous materials (typically obtained from X-ray tomography).

image analysis
porous media
tomography

Python
Shell
Batchfile

PowerSensor3

PowerSensor is a low-cost, custom-built device that measures the instantaneous power consumption of GPUs and other devices at a high time resolution.

GPU
High performance computing

C
C++
Python
+ 3

qumia-train-scripts

Scripts and files related to ML training for the QUMIA project

Machine learning
Neuromuscular
ultrasound imaging

Jupyter Notebook
Python
Shell

ROBIST

Robust Optimization by Iterative Scenario Sampling and Statistical Testing

optimization
python

Python

Rocket

Rocket is a framework for efficient execution of all-pair applications on heterogeneous platforms.

Big data
GPU
High performance computing
+ 1

Java
Cuda
C++
+ 2

Rucio deployment for KM3NeT

This repository contains the Rucio deployment for KM3NeT. It can be used as an example of how to deploy Rucio.

Big data
High performance computing

SalientDescriptor-matlab

If you need to automate your image matching tasks for the purposes of object detection or photo-identification in an easy way, the SalientDescriptor-matlab is right for you

Image processing

MATLAB
HTML

SARXarray

An Xarray extension to process coregistered Single Look Complex (SLC) image stacks acquired by Synthetic Aperture Radar (SAR).

Dask
InSAR
Interferometry
+ 6

ReScript
Python

scriptcwl

Create CWL workflows by writing a simple Python script.

CWL
Workflow technologies

Python
Common Workflow Language

self-hosted runners

Collection of resources to set up GitHub runners on self-hosted infrastructure

High performance computing

Shell
Dockerfile

SimVascular

The only fully open source software package providing a complete pipeline from medical image data segmentation to patient specific blood flow simulation and analysis.

Cardiovascular
Fluid mechanics
Medical image computing
+ 1

C++
Makefile
Python
+ 9

sirup

Sirup is an open-source Python package that makes it easy to connect to, and rotate across, VPN servers provided by services such as ProtonVPN and Surfshark.

ip-rotation
openvpn
python
+ 1

Python
Shell

SlicerIGT

Software toolkit for rapid development of image-guided therapy systems - for minimally invasive medical procedures, where operators rely on computer-generated images rather than direct sight of the target organs.

3D Slicer
deep learning
Medical image computing
+ 2

C++
Python
CMake

snakemake-wrf

A snakemake workflow to run WRF, including pre- and postprocessing. See our blog post for a detailed description.

geospatial
High performance computing
python
+ 1

Jupyter Notebook
Python
Shell